“In a letter he [Alan Johnson] expressed surprise and disappointment over Professor Nutt’s comments which damage efforts to give the public clear messages about the dangers of drugs.

“We remain determined to crack down on all illegal substances and minimize their harm to health and society as a whole.”

Nutt had criticized politicians for “distorting” and “devaluing” the research evidence in the debate over illicit drugs.

Arguing that some “top” scientific journals had published “horrific examples” of poor quality research on the alleged harm caused by some illicit drugs, the Imperial College professor called for a new way of classifying the harm caused by both legal and illegal drugs.

“Alcohol ranks as the fifth most harmful drug after heroin, cocaine, barbiturates and methadone. Tobacco is ranked ninth,” he wrote in the paper from the centre for crime and justice studies at King’s College, London, published yesterday.

“Cannabis, LSD and ecstasy, while harmful, are ranked lower at 11, 14 and 18 respectively.”

Nutt said tonight he was disappointed by the decision but linked it to “political” considerations. “It’s unusual political times, I suppose, elections and all that. It’s disappointing,” he told Sky News. “But politics is politics and science is science and there’s a bit of a tension between them sometimes.”

Nutt clashed with Jacqui Smith when she was home secretary after he compared the 100 deaths a year from horseriding with the 30 deaths a year linked to ecstasy.

Smith also ignored the recommendation of Nutt’s advisory committee that cannabis should not be reclassified from class C back to class B, leading to heavier penalties.

He criticized Smith’s use of the “precautionary principle” to justify her decision to reclassify cannabis and said that by erring on the side of caution politicians “distort” and “devalue” the research evidence.

“This leads us to a position where people really don’t know what the evidence is,” he said adding that the initial decision to downgrade the classification of cannabis led to a fall in the use of the drug.

Nutt acknowledged there was a “relatively small risk” of psychotic illness linked to cannabis use. But he argued that to prevent one episode of schizophrenia it would be necessary to “stop 5,000 men aged 20 to 25 from ever using” cannabis.

Nutt also renewed his support for reclassifying ecstasy from a class A drug to class B, saying the advisory committee “won the intellectual argument” over the issue but obviously didn’t win the decision after the home secretary vetoed the move.

He said the quality of some research papers about cannabis and ecstasy was so poor the articles had to be retracted.

Richard Garside, director of the Centre for Crime and Justice, said Nutt’s briefing paper gave an insight into what drugs policy might look like if it was based on the research evidence rather than political or moral positioning.

Garside added: “I’m shocked and dismayed that the home secretary appears to believe that political calculation trumps honest and informed scientific opinion. The message is that when it comes to the Home Office’s relationship with the research community honest researchers should be seen but not heard.

“The home secretary’s action is a bad day for science and a bad day for the cause of evidence-informed policy making.”